RESEARCH ARTICLE Genomic profiles of Indonesian colorectal cancer patients [version 1; peer review: 2 approved with reservations] Murdani Abdullah 1,2 , Sofy Meilany 3 , Hidayat Trimarsanto 4 , Safarina G. Malik 4 , Ninik Sukartini 5 , Firhat Idrus 1 , Saskia A. Nursyirwan 1 , Virly N. Muzellina 1 , Rabbinu R. Pribadi 1 , Amanda P. Utari 1 , Hasan Maulahela 1 , Ari F. Syam 1 1 Human Cancer Research Center, Indonesian Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia 2 Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia 3 Virology and Cancer Pathobiology Research Center, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia 4 Eijkman Institute for Molecular Biology, Ministry of Research and Technology/National Research and Innovation Agency, Jakarta, 10430, Indonesia 5 Department of Clinical Pathology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia First published: 20 Apr 2022, 11:443 https://doi.org/10.12688/f1000research.109136.1 Latest published: 21 Feb 2023, 11:443 https://doi.org/10.12688/f1000research.109136.2 v1 Abstract Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non- synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this Open Peer Review Approval Status 1 2 version 2 (revision) 21 Feb 2023 view view version 1 20 Apr 2022 view view Ahmad Rusdan Handoyo Utomo , Universitas Yarsi, Central Jakarta, Indonesia 1. Wei Zhang , Northwestern University Feinberg School of Medicine, Chicago, USA 2. Any reports and responses or comments on the article can be found at the end of the article. Page 1 of 15 F1000Research 2022, 11:443 Last updated: 27 NOV 2023